Within natural floodplains, flood disturbances are one of the major events that control ecosystem development and functioning. Our objectives were to better understand the effect of alternate flooding–draining due to tides and/or flooding river regime on riparian soils in terms of bacterial community and nitrate removal. The effect of the frequency and duration of alternate flooding–draining events on redox potential, N removal and soil bacterial community composition was investigated under flooded soils mesocosms for 3, 7 and 14 days, using redox electrode, acetylene inhibition and quantitative real-time PCR techniques. We investigated the dynamics of total, denitrifying and sulfate-reducing bacteria by targeting bacterial 16S rRNA, nosZ and dsrB genes. Alternate flooding–draining conditions increased N removal efficiency compared to the permanently flooded soil and the non-flooded control soil. The redox potential decreased more slowly under alternate flooding–draining than under permanent flooding soils. We evidenced a significant response of the denitrification process to soil type and flood duration. Moreover, alternate flooding–draining had the greatest impact on the soil bacterial and functional groups abundance (nosZ and dsrB genes). This approach by molecular microbial ecology can be performed in addition to the usual soil descriptors and can be considered as a useful indicator.